A motor response control method in a variable charge motion system in which a VCM motor is differentially controlled by a PWM duty regardless of back pressure of intake air in an intake manifold when a current engine rotation speed in revolutions per minute is less than a specific engine rotation speed in revolutions per minute in a VCM position learning state by a controller whereas the VCM motor is differentially controlled by the PWM duty based on the back pressure of intake air in the intake manifold when the current engine rotation speed in revolutions per minute is greater than the specific engine rotation speed in revolutions per minute.